› 5b4k

X-ray diffraction
2.9Å resolution

Crystal structure of the catalytic domain of human PDE10A complexed with N-(4-((5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy)phenyl)-1H-benzimidazol-2-amine

Released:
DOI: 10.2210/pdb5b4k/pdb
PDB entry 5b4k coloured by chain, front view.
PDB entry 5b4k coloured by chain, side view.
PDB entry 5b4k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design and synthesis of potent and selective pyridazin-4(1H)-one-based PDE10A inhibitors interacting with Tyr683 in the PDE10A selectivity pocket.
Yoshikawa M, Hitaka T, Hasui T, Fushimi M, Kunitomo J, Kokubo H, Oki H, Nakashima K, Taniguchi T
Bioorg Med Chem 24 3447-55 (2016)
PMID: 27301679

Function and Biology Details

Reaction catalysed: 
Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195088 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A Chains: A, B
Molecule details ›
Chains: A, B
Length: 338 amino acids
Theoretical weight: 38.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y233 (Residues: 718-1055; Coverage: 32%)
Gene name: PDE10A
Structure domains: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ZN 2 x ZN
Ligand 6DT 2 x 6DT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 49.734Å b: 81.683Å c: 161.654Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.177 0.261
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Computer-aided design of multi-target ligands at A1R, A2AR and PDE10A, key proteins in neurodegenerative diseases.
Kalash et al. (2017)